The DIA pipeline has been quite a #strugglebus

She looked at my blib and Laura’s blib with people from her lab (a.k.a. the Skyline creators)

They found asterisks at the end of some of the blib sequences that could affect Skyline’s ability to peak peaks

Another problem may be that brecan reports the same peptide multiple times, and Skyline doesn’t like that

Overall, this means that my current Skyline output isn’t valid anymore. I can’t work on MSstats or target identification using Skyline data, but I can still look through the literature for proteins of interest. Emma and her team are working on fixing Skyline for our files, so I just have to wait! After everything’s fixed, I will need to check error rates again for the same peptides.